Variant report

Variant	rs12089309
Chromosome Location	chr1:171821340-171821341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10913843	0.90[AFR][1000 genomes]
rs10913896	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10913898	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10913953	0.81[AFR][1000 genomes]
rs12062177	0.85[YRI][hapmap]
rs12064937	1.00[YRI][hapmap]
rs12065857	0.81[AFR][1000 genomes]
rs12087423	1.00[AFR][1000 genomes]
rs12087573	0.85[YRI][hapmap]
rs12093397	0.90[AFR][1000 genomes]
rs12093518	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs28411002	0.90[AFR][1000 genomes]
rs7527401	0.90[AFR][1000 genomes]
rs7535018	0.85[YRI][hapmap]
rs7554281	1.00[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171812200-171833200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:171814600-171833400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:171819600-171832800	Weak transcription	Left Ventricle	heart
4	chr1:171820000-171822200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:171820200-171821600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:171820200-171832600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:171820400-171821400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:171820400-171821600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:171820400-171822000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:171820400-171822400	Enhancers	NHDF-Ad	bronchial
11	chr1:171820600-171827600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:171820800-171821800	Weak transcription	HSMMtube	muscle
13	chr1:171821000-171821800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:171821200-171822000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:171821200-171822000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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